|3/19||Solutions to Problem Set 4 have been posted: ppt pdf. We recommend the PowerPoint slides because they include explanatory notes.|
|3/13||The Friday 3/14 Problem Session is cancelled. Solutions to Problem set 4 will not be presented on Friday since not everyone will have turned in their solutions. Instead, we will release the solutions on the website once everyone's solutions are in.|
|3/12||Problem set 4 is due! Please either turn it in in class or email it to firstname.lastname@example.org by 12:50 pm.|
|3/5||A scribing slot has opened up for March 10. If you would like to scribe this lecture, please email email@example.com.|
|3/5||Problem set 3 has been graded! Come pick them up during officer hours, problem sessions, or lecture.|
|2/27||Problem set 4 has been posted.|
|2/27||Problem set 3 is due! Please either turn it in in class or email it to firstname.lastname@example.org by 12:50 pm.|
|2/22||Problem set 2 has been graded! Come pick them up during officer hours, problem sessions, or lecture.|
|2/13||Problem set 3 has been posted.|
|2/13||Problem set 2 is due! Please either turn it in in class or email it to email@example.com by 12:50 pm.|
|2/11||There was a mistake in the formulas in PS2 problem 1.c.iii. The formulas given in lecture are correct - please see the updated pdf.|
|2/6||Problem set 1 has been graded! Come pick them up during officer hours, problem sessions, or lecture.|
|2/2||Update: Slot filled! A scribing slot has opened up for March 3. If you would like to scribe this lecture, please email firstname.lastname@example.org.|
|1/30||Problem set 1 is due! Please either turn it in in class or email it to email@example.com by 12:50 pm.|
|1/30||Problem set 2 has been posted.|
|1/19||Scribing assignments have been made for all lectures.|
|1/16||Problem set 1 has been posted.|
|1/10||There will be no problem session on Friday January 11.|
|1/10||If you need help finding a group for collaborating on the problem sets, please email firstname.lastname@example.org with a request.|
|1/10||If you would like to scribe one of the lectures, please email email@example.com with the date you would like.|
CS161: Design and Analysis of Algorithms, or equivalent familiarity with algorithmic and data structure concepts.
Durbin, Eddy, Krogh, Mitchison "Biological Sequence Analysis"
Gusfield "Algorithms on Strings, Trees, and Sequences"
Homework. Course will be graded based on the homeworks, NO FINAL. The course will have four challenging problem sets of equal size and grading weight. These must be handed in at the beginning of class on the due date, which will usually be two weeks after they are handed out. Recognizing that students may face unusual circumstances and require some flexibility in the course of the quarter, each student will have a total of three free late days (weekends are NOT counted) to use as s/he sees fit. Once these late days are exhausted, any homework turned in late will be penalized at the rate of 20% per late day (or fraction thereof). Under no circumstances will a homework be accepted more than three days after its due date.
Late homeworks should be turned in to a member of the course staff, or, if none are available, placed under the door of S266 Clark Center. You must write the time and date of submission on the assignment. It is an honor code violation to write down the wrong time.Students with biological and computational backgrounds are encouraged to work together.
Scribing. Optionally, a student can scribe one lecture. Lecture notes will be due one week after the lecture date, and the grade on the lecture notes will substitute the two lowest-scoring problems in the homeworks. To ensure even coverage of the lectures, please sign up to scribe beforehand with one of the course staff.
Students may discuss and work on problems in groups of at most three people but must write up their own solutions. A student can be part of at most one group. If a student works individually, then the worst problem per problem set will be dropped. When writing up the solutions, students should write the names of people with whom they discussed the assignment. Also, when writing up the solutions students should not use written notes from group work.
Students are expected not to look at the solutions from previous years. Copying or intentionally refering to solutions from previous years will be considered an honor code violation.
Problem Sessions (optional): Friday 1:15 - 2:05 pm in McCullough 115
Office: Clark Center S266
Office hours: Monday 2:15 - 3:30 pm in Clark Center S266
Phone: (650) 723-3334
Email: ude.drofnats@mifares (written backwards to avoid spam)
Office: Clark Center S260
Office hours: Thursdays noon - 2 pm in Clark Center S260
Phone: (650) 725-6094
Office: Clark Center S260
Office hours: Tuesdays 1 - 3 pm in Gates B24A (phone during office hours: (650) 725-4385)
Phone: (650) 725-6094 (except during office hours)